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(-) Description

Title :  CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
 
Authors :  F. J. Medrano, A. Romero
Date :  05 May 13  (Deposition) - 15 Jan 14  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Oxidoreductase, Class Ii (Fungal) Peroxidases, Protoporphyrin Ix, Electron T Lignin Peroxidase, Lignin Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Fernandez-Fueyo, F. J. Ruiz-Duenas, M. J. Martinez, A. Romero, K. E. Hammel, F. J. Medrano, A. T. Martinez
Ligninolytic Peroxidase Genes In The Oyster Mushroom Genome: Heterologous Expression, Molecular Structure, Catalytic And Stability Properties, And Lignin-Degrading Ability.
Biotechnol. Biofuels V. 7 2 2014
PubMed-ID: 24387130  |  Reference-DOI: 10.1186/1754-6834-7-2

(-) Compounds

Molecule 1 - MANGANESE PEROXIDASE 4
    ChainsA, B
    EC Number1.11.1.13
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainK-12
    Expression System Taxid316407
    Expression System VariantW3110
    Organism CommonOYSTER MUSHROOM
    Organism ScientificPLEUROTUS OSTREATUS
    Organism Taxid5322

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 29)

Asymmetric Unit (4, 29)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CIT2Ligand/IonCITRIC ACID
3HEM2Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO421Ligand/IonSULFATE ION
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CIT1Ligand/IonCITRIC ACID
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO410Ligand/IonSULFATE ION
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CIT1Ligand/IonCITRIC ACID
3HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE
4SO411Ligand/IonSULFATE ION

(-) Sites  (29, 29)

Asymmetric Unit (29, 29)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:49 , GLY A:67 , ASP A:69 , SER A:71 , HOH A:2119 , HOH A:2133BINDING SITE FOR RESIDUE CA A 401
02AC2SOFTWARESER A:177 , ASP A:194 , THR A:196 , ASP A:199 , ASP A:201BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREHIS A:40 , GLU A:41 , ARG A:44 , PHE A:47 , GLU A:147 , PRO A:148 , LEU A:172 , LEU A:173 , SER A:175 , HIS A:176 , ALA A:179 , ALA A:180 , GLN A:181 , ASP A:182 , THR A:183 , ILE A:184 , PHE A:193 , LEU A:235 , SER A:237 , MET A:269 , HOH A:2093 , HOH A:2094 , HOH A:2377BINDING SITE FOR RESIDUE HEM A 500
04AC4SOFTWAREASP B:49 , GLY B:67 , ASP B:69 , SER B:71 , HOH B:2108 , HOH B:2120BINDING SITE FOR RESIDUE CA B 401
05AC5SOFTWARESER B:177 , ASP B:194 , THR B:196 , ASP B:199 , ASP B:201BINDING SITE FOR RESIDUE CA B 402
06AC6SOFTWAREHIS B:40 , GLU B:41 , ARG B:44 , PHE B:47 , GLU B:147 , PRO B:148 , LEU B:172 , LEU B:173 , SER B:175 , HIS B:176 , ALA B:179 , ALA B:180 , GLN B:181 , ASP B:182 , THR B:183 , ILE B:184 , PHE B:193 , LEU B:235 , SER B:237 , MET B:269 , HOH B:2083 , HOH B:2097 , HOH B:2142BINDING SITE FOR RESIDUE HEM B 500
07AC7SOFTWARESER A:5 , LYS A:6 , HOH A:2003BINDING SITE FOR RESIDUE SO4 A1339
08AC8SOFTWAREGLU A:34 , CYS A:35 , HOH A:2081 , HOH A:2293 , HOH A:2401BINDING SITE FOR RESIDUE SO4 A1340
09AC9SOFTWARELYS A:62 , PHE A:63 , HOH A:2167 , HOH A:2608BINDING SITE FOR RESIDUE SO4 A1341
10BC1SOFTWAREGLY A:294 , ARG A:295 , HOH A:2524 , HOH A:2609BINDING SITE FOR RESIDUE SO4 A1342
11BC2SOFTWAREARG A:295 , LYS A:297 , GLN A:298 , HOH A:2529 , HOH A:2532BINDING SITE FOR RESIDUE SO4 A1343
12BC3SOFTWAREALA A:303 , THR A:328 , PHE A:329 , HOH A:2536 , HOH A:2539 , HOH A:2588BINDING SITE FOR RESIDUE SO4 A1344
13BC4SOFTWARELYS A:316 , GLY A:327 , THR A:328 , HOH A:2610 , LYS B:101BINDING SITE FOR RESIDUE SO4 A1345
14BC5SOFTWARELYS A:281 , HOH A:2068 , ARG B:321 , PRO B:323 , HOH B:2537BINDING SITE FOR RESIDUE SO4 B1339
15BC6SOFTWAREARG A:321 , PRO A:323 , HOH A:2576 , HOH A:2579 , LYS B:281 , HOH B:2058BINDING SITE FOR RESIDUE SO4 A1346
16BC7SOFTWAREHOH A:2251 , THR B:328 , PHE B:329 , THR B:330 , HOH B:2330 , HOH B:2500 , HOH B:2550BINDING SITE FOR RESIDUE SO4 B1340
17BC8SOFTWAREASP B:325 , LYS B:326 , HOH B:2540BINDING SITE FOR RESIDUE SO4 B1341
18BC9SOFTWAREALA B:303 , THR B:328 , PHE B:329 , HOH B:2501 , HOH B:2506 , HOH B:2547BINDING SITE FOR RESIDUE SO4 B1342
19CC1SOFTWAREASN A:12 , ILE A:283 , ASP A:284 , HOH A:2029 , HOH A:2031 , HOH A:2509BINDING SITE FOR RESIDUE SO4 A1347
20CC2SOFTWAREASN B:12 , ILE B:283 , ASP B:284 , HOH B:2024 , HOH B:2476 , HOH B:2571BINDING SITE FOR RESIDUE SO4 B1343
21CC3SOFTWAREARG B:126 , GLU B:287 , HOH B:2480 , HOH B:2482BINDING SITE FOR RESIDUE SO4 B1344
22CC4SOFTWARELYS A:101 , LYS B:316 , GLY B:327 , THR B:328 , HOH B:2429 , HOH B:2572 , HOH B:2573 , HOH B:2574BINDING SITE FOR RESIDUE SO4 B1345
23CC5SOFTWAREASP A:325 , LYS A:326 , HOH A:2580 , HOH A:2614BINDING SITE FOR RESIDUE SO4 A1348
24CC6SOFTWARELYS B:62 , PHE B:63 , HOH B:2153 , HOH B:2576BINDING SITE FOR RESIDUE SO4 B1346
25CC7SOFTWAREARG B:126 , HOH B:2450 , HOH B:2577 , HOH B:2578BINDING SITE FOR RESIDUE SO4 B1347
26CC8SOFTWAREGLY B:294 , ARG B:295 , HOH B:2490 , HOH B:2579BINDING SITE FOR RESIDUE SO4 B1348
27CC9SOFTWAREARG B:295 , LYS B:297 , GLN B:298 , HOH B:2492 , HOH B:2497BINDING SITE FOR RESIDUE SO4 B1349
28DC1SOFTWAREILE B:215 , PRO B:216 , PRO B:230 , GLY B:231 , HOH B:2354 , HOH B:2386 , HOH B:2402 , HOH B:2404 , HOH B:2580 , HOH B:2581 , HOH B:2582BINDING SITE FOR RESIDUE CIT B1350
29DC2SOFTWAREILE A:215 , PRO A:216 , PRO A:230 , GLY A:231 , HOH A:2389 , HOH A:2422 , HOH A:2439 , HOH A:2441 , HOH A:2615 , HOH A:2616 , HOH A:2617 , HOH A:2618BINDING SITE FOR RESIDUE CIT A1349

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:4 -A:16
2A:15 -A:285
3A:35 -A:121
4A:249 -A:314
5B:4 -B:16
6B:15 -B:285
7B:35 -B:121
8B:249 -B:314

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4BM1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BM1)

(-) Exons   (0, 0)

(no "Exon" information available for 4BM1)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:337
 aligned with W5IDB6_PLEOS | W5IDB6 from UniProtKB/TrEMBL  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         W5IDB6_PLEOS     2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
               SCOP domains d4bm1a_ A: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee...hhhhh.ee.........hhhhhhh...............ee........eehhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.hhhh................hhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bm1 A   2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       

Chain B from PDB  Type:PROTEIN  Length:337
 aligned with W5IDB6_PLEOS | W5IDB6 from UniProtKB/TrEMBL  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
         W5IDB6_PLEOS     2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
               SCOP domains d4bm1b_ B: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.........ee...................hhhhhhhhhhhhh.hhhhhhhhhhhhhh.ee...hhhhh.ee.........hhhhhhh...............ee........eehhhhhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhee.hhhh................hhhh............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4bm1 B   2 AKCSKGRTASNDACCVWFDVLDDIQENLFDGGECGEEVHESLRLTFHDAIGFSPALTRQGKFGGGGADGSIMLFSDIETNFAANNGVDDIVEQQKPIAIKHQVSFGDFIQFAGAVGSSNCAGGPRIQFLAGRSNVTKPSPDHLVPEPFDSVTSILARMGDAGFKPDEVVALLASHSVAAQDTIDPKLAGHPFDSTPSDFDSQFFVETLLKGTLIPGDSLHKGQVKSPLPGEFRLQSDELLARDSRTSCEWQSFISNPNSMVPKFERAMAKMATLGQNPKKLIDCSEVIPVPRGRVKQPTLPAGKTIKDIEASCRKAPFPRLPTDKGTFTSILPVPSS 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BM1)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (W5IDB6_PLEOS | W5IDB6)
molecular function
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0004601    peroxidase activity    Catalysis of the reaction: donor + hydrogen peroxide = oxidized donor + 2 H2O.
biological process
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        W5IDB6_PLEOS | W5IDB64bm2 4bm3 4bm4

(-) Related Entries Specified in the PDB File

4blk CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM I
4bll CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II
4bln CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III
4blx CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV
4bly CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM V
4blz CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VI
4bm0 CRYSTAL STRUCTURE OF FUNGAL VERSATILE PEROXIDASE I FROM PLEUROTUS OSTREATUS - CRYSTAL FORM VII
4bm2 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM II
4bm3 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM III
4bm4 CRYSTAL STRUCTURE OF MANGANESE PEROXIDASE 4 FROM PLEUROTUS OSTREATUS - CRYSTAL FORM IV